Thoughts
by calathiel94
Summary: After so long of denying themselves each other, will the two leaders finally give in to their love? John/Elizabeth, I suck at summaries :\
1. Chapter 1

**Disclaimer:** I don't own Stargate Atlantis, if I did, a LOT would be different. All rights to their respective owners, etc..

**A/N:** I wrote this like 2 years ago so it's not my best work, however I did have a read through and I don't think it turned out TOO badly. This was my first fic I ever wrote... enjoy!

Elizabeth sat back in her office chair, her arms folded tightly across her chest. She let out an exasperated sigh, hanging her head. _Why?_ Why was she feeling like this? She knew the rules – well, her own personal ones – _never date your subordinates,_ and it was damn well clear that what she was feeling wasn't exactly 'appropriate'. Elizabeth squeezed her eyes shut tight. Nothing seemed to make sense to her anymore, things had change and she wasn't sure whether it was for the better or worse. She knew she shouldn't be feeling this way. If things escalated and someone back on Earth found out, she would be instantly out of her job. Or worse yet, _he_ could be transferred, away from Atlantis, his home. _Away from me..._ Elizabeth snapped her head up, quickly dismissing the thought. No! This wasn't about her. She couldn't jeopardise the city, his part in the whole expedition had saved them too many times.

Elizabeth propped her elbows up on the desk, resting the bottom of her chin in her palms. She concentrated on her breathing for a few moments, trying to distract herself from her perilous thoughts. She glanced around her office, taking in the laptop in front of her, the stacks of mission reports on her desk. She looked at the wooden pot he had given her for her first birthday in Atlantis; that pot that had its rightful place on the corner of her desk only for her to hold some memories by, memories that centred on a particular Colonel of the Air Force. Elizabeth shook her head again. She had to stop thinking about him! She had to stop thinking about that messy black hair that seemed untameable; those deep brown eyes that met her green ones; that cheeky schoolboy smile that always made her heart flutter... Elizabeth groaned aloud and massaged her temples almost to the point of where the action was growing painful. Anyone could see that she was growing weary of the whole situation.

"For crying out loud Elizabeth, you're acting like a teenager with her first crush!" she scolded herself, determined now to focus on something else. In the end, she stared at her desk, seemingly marvelling at the craftsmanship. Her eyes drifted over it a few times before settling on the left corner furthest from her. She immediately thought of John. That was where he usually sat, perched at the end of the desk when he wanted something he knew he would have to sweet talk her into. The thought of him made her smile contentedly, making her temporarily forget about the reports that were waiting for her to read.

Elizabeth sighed again. She obviously wasn't going to stop thinking about him any time soon. She decided to stop being so smitten about the whole thing, and decided to focus on the more... difficult parts of their relationship. The parts that prevented her from just going where her heart wanted to go so badly.

Technically, she wasn't actually _breaking_ her rules; there was just a number of growing feelings involved that shouldn't be. But she couldn't just _ignore_ those feelings. That much was abundantly clear now as those unspoken feelings had developed to the point where she couldn't help but think about him every few seconds.

Elizabeth was trying to clear her thoughts. She inhaled deeply for a few moments, before sighing in frustration, folding her arms and placing them on the desk in front of her. She rested her head gently on her forearms and her eyes fluttered closed. She began to think about just how things had happened. How she had come to realise her true feelings for him, discovering for herself that this thing between them was more than an attraction, it something deeper that made her heartbeat quicken and her soul feel alive. Admittedly, there was a connection between them from the start, a bit like an animal attraction. It wasn't until the end of their third week in the great city that she began to realise that what they had was deeper than an attraction.

It was when the Stargate had engaged and they were awaiting his team's arrival. Elizabeth was already worried at that point; she had received by radio that an alien bug had attached itself to John's neck. Ford was unable to remove it despite his best efforts, and then the jumper got stuck halfway through its return to the 'gate. There was no way they could get back through at the time, and the bug was slowly killing John. Elizabeth had never felt more distraught in her entire life. It was later, when they were safely back in Atlantis and she had been called to the jumper bay that she truly realised her feelings for him. When she had seen his body lying there, with Carson trying to resuscitate him, she had to fight to hold back her tears. This man meant so much to her, it was strange really, that it had taken until that moment for her to apprehend it; stranger even that her heart was yearning for him after such a short time of knowing him.

Of course, after that their relationship and their bond just kept growing. Like all people, they had their ups and downs, but it only made them stronger in the end. The incident with the Genii had only increased their chemistry and feelings for each other further. It was when she saw the emotion in John's eyes after he had rescued her from Kolya that she understood he felt the same things for her as she did for him. When he had taken her hand and led her back to the control room, she had never felt safer, more secure with a single person than she had in a long time.

It was only a few months after that when the Wraith's siege on Atlantis began. So much happened in those few days; it made Elizabeth finally understand the extent of her feelings for John. When she had reluctantly approved of his suicide mission, she had nearly broken down in tears. She was sending the man that made her whole to his death; the man that had made her appreciate so many things in life; the man who had taught her how to _love._ Just watching the dot on the sensors that indicated him broke her heart. When she thought he had died, she felt her heart shatter into a million pieces. She just wanted to curl up and die so that she could be with him again. It was only a few minutes later that Elizabeth heard his voice over the radio, all her hopes that had been diminished made her come back to life, made her feel, made her _want_ to tell him exactly how much he meant to her. But when it came to it, words just couldn't express how she felt. It was all she could do to lock her eyes with his without breaking down in tears, before pulling him into an embrace that conveyed just the turmoil her heart had been without him, with the uncertainty of whether she would be able to see him just one last time.

It was from that moment onwards that she knew she loved this man more than anything in the world, and that she would do anything for him.

Elizabeth sighed once more, standing up from her desk and pacing around her office. It was late, way past two in the morning, and she knew she needed to sleep. She needed to sleep on the clot of emotions building up in her heart, to once more keep them on hold until the morning before that inner battle and restraint began once more. Closing her eyes and breathing in deeply, she stepped out of her office on the way to her quarters.

She paused outside John's room and pondered whether she should knock. She wondered what would happen if he answered, and just how he would react if she kissed him there and then; if she could feel his body pressed to hers, be able to voice the extent of her inner feelings and stay wrapped in his embrace until the morning, just what would happen then?

Smiling slightly to herself, Elizabeth continued walking to her room. One can only dream.

**A/N2: **There are 2 more chapters to come up, there WILL be a happy fluff filled ending! Please review, it feeds my muse. :]


	2. Chapter 2

**Disclaimer: **I do **not** own Stargate Atlantis; I am merely borrowing their characters. All rights belong to their respective owners.. Don't sue, this is purely entertainment!

**A/N: **A **big** thank you to Scotius andPuddle-Jumper38 for reviewing; this chapter is up just for you guys!

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John tossed over in his bed. He looked at his watch – it was 1:38 in the morning and he still couldn't sleep. Not with what was on his mind. She was always on his mind, gnawing at him every day. She clouded his thoughts at the least helpful of times; she made his heart strain at the distance they put between themselves. She was so close to him, yet so far out of reach. _She is the woman I love,_ John thought sadly to himself, his heart once more crying out for her touch_._ People said love was easy; you could just fall in and out of it in the blink of an eye.

"If only..." John muttered to himself, letting slip an agitated sigh. Those people obviously didn't know what true love was. He loved this woman, loved her so much that whenever he wasn't with her a part of him felt like he was dying. She was what he lived for, in hope that one day things would be different. Things would never be simple with Elizabeth; there was too much against them. His work in the military had him constantly being drawn away from her due to other responsibilities, and her roll leading the city... well that goes without saying.

With each thought that passed, John got angrier and angrier. Nothing made much sense anymore. Love. Justice. None of it was _fair._ He threw hard punches at his pillow in attempt to rid himself of some of the hostile emotions, his mood worsening every time he swung.

"Damn it!" he swore, "Damn it all!" He felt like trashing his room, and as juvenile as it sounded, it deemed rather appealing. John knew he was being immature. So he did what he always did to burn off his rage – go for a jog around the city, overwork himself and get lost in his thoughts.

John roughly pushed himself up from his bed, not bothering to change. He was in his grey jogging bottoms and black vest, his hair messy and feet bare. He wandered out of the living quarters and down the hallway, going to one of the newly discovered parts of the city. Spots like these are where he usually went to calm himself, as no one would be there, at least this early in the morning.

John broke into a comfortable jog, building up speed until he was practically sprinting. Already, he began to feel some of the stress he had experienced earlier exit his body. John worked on his breathing, before letting his thoughts drift back to the first time he noticed he had feelings for her.

There had always been an attraction between them, right from the start. John couldn't believe it when he had been fortunate enough to land a position in Atlantis, let alone get to work alongside this beautiful woman. There was a lot of playful flirting at the start, but he didn't think it was much deeper than that. But a few months after the expedition team had settled into Atlantis, the Genii launched an attack on their beloved city. John cursed himself for not being in the gate room at that time, and when he heard over radio that Kolya had Elizabeth, he was practically kicking himself for not being there for her. Frustrated as he was, John couldn't take much more stress. It was when Kolya informed him that he had killed Elizabeth that John snapped. He was hell-bent on revenge, not letting anything stop him in his attempts to avenge his leader. With the sudden declaration that she was actually _alive,_ John felt like a weight had been lifted from his chest. When he finally reached the gate room, he was so close to losing her that he was actually scared. He took a chance and shot Kolya, quickly running to Elizabeth's aid. He was concerned for her well being, but knew that she would recover quickly. John took her hand and led her up the stairs to the control room. It was at that very moment he knew that this woman meant so much to him, that if he lost her, he would lose a part of himself, and he took it upon himself to protect her as best as he could, even if it meant with his life.

John's legs were killing him, his muscles burned, his breathing was quick and desperate, his lungs were on fire, his heart felt like it was going to explode at any moment and his clothes were drenched in sweat. But he still kept on running. He knew this pain wasn't near enough as excruciating to what his heart was feeling, but somehow it felt like he was proving his credibility to Elizabeth in some kind of way. It wasn't until his legs buckled beneath him that he knew he'd done more than enough. John glanced at his watch that slipped down his sweaty arm. 2:24. He'd been running for 43 minutes straight at a ridiculously fast speed. _Now if that wasn't credibility then I dunno what is,_ John silently declared before heading back to his quarters.

He stepped into his room. As much as he hated to admit it, he stank and was in desperate need for a shower. He stripped quickly and left his clothes in a pile by the bathroom door. John turned the shower on to a low temperature, basking at the feel of the cold needles against his clammy skin. John sucked in a deep breath and closed his eyes, resting his head against the shower wall. He concentrated once more on his thoughts. Love. This is what it all came down to. He had refused to believe it at first, but right now it all made perfect sense. He was in love, and he had only _really_ thought about is seriously now.

"Love is blind..." he whispered truthfully. Because it was. He'd never thought that he would fall in love with Doctor Elizabeth Weir and yearn for her day and night. Hell, he'd never even thought he'd make it past Captain in the air force, let alone travel to a complete different Galaxy away from home and everyone he knew. His thoughts once again travelled back to Elizabeth. He didn't scold himself for thinking about her in this way as he was sure she did. Being as perceptive as John Sheppard did have its advantages after all. He couldn't help but smile at the thought of those sparkling green eyes, her short locks of brown curly hair, the way her eyebrow quirked up whenever she was flirting with him, the way she giggled like a schoolgirl with Teyla whilst watching him across the mess hall and making ridiculous attempts to conceal her stares. He knew he loved this woman. He'd loved her since he'd first laid his eyes on her, loved her for every decision she'd ever made, loved her for taking him on despite his track record. But most of all, he loved her for loving him.

John got out the shower, still deep in his thoughts. It was 2:43 now and he knew he wouldn't be able to sleep. He contemplated on what he was going to do next. He dressed into his spare set of pyjamas, again not bothering to put on his boots put instead slipping on some socks. John stood for a moment, obviously having an internal battle of wills. It seemed that one side of the war had won, and he stood up straight, taking a few calming breaths before walking out of his room.

He knocked quietly on the door only a few paces away from his room. There was a muffled response, carried by an agitated voice that told him the occupant was now awake, but not too pleased about it. John swallowed, dreading what would happen if he dared knock again. He sighed, stood up straight and knocked again, this time louder.

"Hello?" he called quietly, not wanting to wake the other members of the expedition. He paused for a moment before continuing. "It's me, John. We need to talk about...us."

He shifted uneasily from one foot to the other. He'd had his little speech all planned out, yet it seemed to have dispersed into nothing when he had actually come to saying it. There were a few muffled noises from inside and disgruntled groans, before the door opened. She looked as beautiful as ever.

Elizabeth was slightly shorter than John, with long locks of curly brown hair tucked behind her ears. Her green eyes lit up when she saw him and her lips twitched upwards into a half smile. An eyebrow lifted quizzically as he leant lazily against the door frame and flashed his trademark schoolboy grin at her.

John reached out and gently tucked a stray lock of hair behind Elizabeth's ear, before his expression grew serious and he opened his mouth to speak.

"Do you mind if I come in? I think it's about time we talk and I'd rather it stayed quiet..." he smiled again, this time a lot more nervous. Elizabeth smiled back, knowing that the Colonel wouldn't have disturbed her this early in the morning if he didn't have a reason.

She stepped back and gestured for John to enter.

The door slid shut behind them.

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A/N2:

I'm not one for cliffys so I don't think this is too bad lol, remember to review! Next chapter should be up when I have time within the next few days. :] 


	3. Chapter 3

**A/N: **Thanks to everyone who has reviewed so far! Final chappy. :]

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"So, what can I do for you at this fine hour of the morning?" Elizabeth asked, her tone playful but with underlying seriousness to it. She was still half asleep and it showed, as she kept feeling the need to blink and finding it difficult to focus for more than a few seconds.

"Oh, you know, just checking that you're in bed and not overworking yourself, that kinda thing. We've had a busy week and all, I was just a little concerned..." John replied. This was bad. This was a really, really bad idea. He shouldn't have come, he knew that much now. His own words sounded nonsensical to John as they were probably conjured up by some redundant part of his brain. The rest of his brain seemed to have shut down upon seeing the love of his life. God she was beautiful, bed hair and all!

Trying to avoid eye contact as he thought he had messed up just by being there, John looked around her room. He'd only ever seen it when they were checking out all the living quarters. She'd certainly changed the place.

"Oh really?" She took a step towards John, part of her smiling, the other part glowering. He realised she was about to go into a full blown lecture on the privacy of others, mainly because she hadn't appreciated the intrusion of her sleep. "John, I really don't think you need to be _checking up_ on me. First of all that is an invasion of my privacy. Who knows what I could have been doing in here?" A grin broke onto John's face and it took a moment for Elizabeth to register what she had just said. She rolled her eyes at his childish behaviour but couldn't help but smile slightly. She coughed and got back to what she was saying. "As I was saying, I'm fine. I was awoken this very hour by my military commander, who was concerned as to whether I was getting enough rest. Usually, I would admire the gesture. But how do you expect me to _sleep_ if I get woken up at this ungodly hour of the morning? Now I would _really_ appreciate it if you–" she never managed to finish what she was saying, as John had closed the space between them and kissed her. It was only a quick brush against her lips, his own lingering there for a few more moments before they broke apart.

"You were saying?" John breathed quietly, his brown eyes locked with her green. Elizabeth held his gaze for a moment before placing both of her hands on his cheeks and kissing him again, this time more intense than their first.

John instinctively placed his hands on her waist, one of them travelling to the small of her back and resting there whilst the other moved up to her hair. He started playing about with it, twisting it between his fingers before letting his hand travel back down to her waist. Elizabeth moved one hand to his neck, holding on to him as her other hand found his unruly hair. Her fingers brushed through it, scratching at his scalp.

She deepened the kiss, letting slip a small moan of pleasure. She felt John smile against her lips as he broke apart from her and began kissing down her neck. More moans and gasps escaped her. Before John knew what was going on she threw him backwards and onto the bed, immediately kissing him again, this time more passionate. By this time she was demanding entry to his mouth, and it was granted almost instantly. She delved her tongue into his mouth, exploring him so that she knew every part of him, so that she knew his taste, his feel.

Elizabeth pulled them apart, taking off his shirt and trailing kisses all over his torso. John let out a small moan before flipping her over onto her back and beginning to kiss her again. Elizabeth closed her eyes, hardly believing how lucky she was to be with this man. The rest of the night passed in intimate ecstasy, their love for each other expressed through their eyes and actions. Their lovemaking was beyond rapture, and Elizabeth felt like the happiest woman alive.

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Elizabeth woke up with strong arms around her. She was still naked, as was John. They had fallen asleep in each other's arms, but during the night they had obviously shifted positions so he was now spooning her from behind. The covers were pulled up above them, exposing only their feet and upper bodies poking out of either end.

Elizabeth slowly rolled over, careful not to wake him. She was facing him now, watching him sleep. He looked so peaceful. She closed her eyes again, snuggling into his chest and breathing in his scent. She smiled to herself. No regrets.

Elizabeth remained like this for a long time before propping up gently onto one of her elbows. She studied John's face, taking a mental picture that she would always remember.

Eventually she saw John open one of his eyes sleepily; he took in his surroundings before focusing on Elizabeth, a smile creeping onto his face. She smiled warmly back at him.

"Morning sleepy," she said quietly, taking in his features. She leant forward and gave him a gentle kiss on the lips before pulling back and looking at him again. Elizabeth smiled to herself, her eyes drifting over his face before settling on his hair. It hadn't seemed to have changed much during the night; if possible it was slightly messier. That fact in itself was one of the things she loved about John Sheppard – his untameable hair. Strange as it sounded, it was a trait that only he had; his hair was unique, no one else she had ever met had hair like him. That just made him all the more special to her.

"What?" John gave her a puzzled look.

"What do you mean 'what'?" Elizabeth broke from her thoughts, meeting his confused gaze and raising an eyebrow in response.

"I mean, why do you keep looking at me like that? Is there something on my head?" he was grinning at her now, catching on to why she was staring at him. Nevertheless, he ran his fingers through his hair, trying to tidy it up before giving her his best puppy dog pout, knowing he would get a response. "C'mon, you can tell me. Nothing to be embarrassed about." He gave her a wink, flashing another grin at her, before returning to his pout. Elizabeth laughed, obviously finding the whole thing amusing. She ran her fingers through his hair before speaking.

"Well, I was just telling myself how sweet it is when you sleep; you really do snuggle up to anything close to you. And bed hair on you? It's the cutest thing." Elizabeth was teasing him now, John knew that. Still, he sat up feigning hurt.

"Cute? I most certainly am not anything even _close_ to cute, fluffy or sweet when I sleep!" he shot back, his eyes lighting up into a smile.

"Ok, well would your male bravado prefer it if I told you that you snore like a pig? That really is _not_ amusing." Elizabeth winked at him cheekily before sitting up in bed. John raised his hands in defeat, shifting into a sitting position against the back of his bed and letting Elizabeth snuggle up on his right side.

John closed his eyes momentarily, letting the dark brown bob of hair cuddle into his side. She rested her head on his collarbone, wrapping her arms around his waist and sighing peacefully. John took in the smell of her hair. It was a flowery scent, lavender perhaps? He registered this scent in his brain as that of Elizabeth, of their first night together. He would love that smell for all of eternity, that much he knew.

As they lay there together, John thought about them, about what they had become. On their journey they had started off as strangers, developed their relationship to friendship. That then progressed to an even closer bond, that of soul mates. And now they were lovers, forever in one another's hearts.

"Elizabeth?" John questioned, looking down at the beauty he had cradled in his arms.

"Hmmm?" she replied, rubbing her head against his chest.

"Elizabeth. For a long time now I've been having these... feelings, for you. I usually find it... hard... to talk about my feelings. But with you, I just feel like I can share anything with you. Despite things I may have said and done in the past, I realise that, well, I uh... I love you, Elizabeth. I love you with all my heart and without you I honestly don't know what I would do with myself. So... thank you. Thank you for everything, and I just felt that you should know how I feel..." John finally stopped talking. Now _that_ had been harder than he'd expected. So many things to say, yet he always failed to find the words to describe them to her. This beautiful woman was breaking down his vocabulary, until only one word remained: love.

Elizabeth had raised her head somewhere in his speech, listening intently. Of course she knew how he felt. She felt the exact same thing, she knew she had to say something, but she couldn't. Her eyes brimmed with tears at his declaration. She knew it had come straight from his heart; she saw it in his eyes. Elizabeth smiled, leaning forward and kissing him passionately.

When they broke apart, Elizabeth looked deep into his eyes and took his hand.

"John, you know I love you. I think I've loved you for so long now that it felt like my heart would rip out if I didn't see you. It was hard for me, not being able to say how I felt. God, it was the hardest thing I've ever had to deal with, and I have gone through a _lot._ Thing is, I love you so damn much, that now we're at this stage of our relationship... I really don't know what can happen. But we'll have to deal with whatever comes our way, and together, I know we can make it through anything." She finished speaking, her gaze never leaving John's.

After a few more moments of just lying there, looking at each other, John smiled.

"Together," he spoke softly, "Together, we can do this. We can do _anything_ if we set our minds to it. Just you and me, Elizabeth. Forever." With that, he trailed off, kissing her deeply and intently, before once more pulling her into his arms, never wanting to let go.

_This, John._ He thought tenderly to himself. _This is what love is._

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**A/N2:** See that big button underneath that says 'review'? Please click it and leave a comment, even a little one! This is the final chapter and I don't plan on writing any more so just give me your thoughts on the fic, flames or good comments I honestly don't mind! It will make me happy :p


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